Stock up with some weapons or talk with the locals. Either way, you can't get the psycrystal near the graveyards until you have Reveal. You also learn a guy named Zack was listening to Madra. Sure they did Madra harm, but they didn't expect them to follow them into Alhafra. He'd intent to find Briggs, who is in the boat of East-Alhafra. So, just hop over there. When you see the ship, it's totally broken. But you can fix it later. Enter the boat now and you'll see Zack chatting with Briggs. They aren't very clever, and Jenna says so. This means the begin of a tough battle. You could go to Airs Rock first, in order to train a bit. If not, here we go:

BRIGGS
Max. HP	Main Attacks	Weakness	Resistance	Exp. Pts	Coins	Drops
984	Fysical Attacks, Signal Whistle	All	None	?	?	?

SEAFIGHER
Max. HP	Main Attacks	Weakness	Resistance	Exp. Pts	Coins	Drops
197	Use of Bramble Sead, Oil Drop Fysical Attacks	All	None	?	?	?

Focus your summons, djinn and psynergy on Briggs, as he can call out another pirate everytime, which is defintly annoying. Be careful of the seafighters though, as they can give you lots of damage, when using a Oil Drop or a Bramble Seed. Heal frequently to stay in top-shape. It's handy to use so now and then a summon, then a psynergy with a wide range like Beam or Earthquake, then use an individual attack or psynergy. I hoped you stocked up at least with some herbs or having the Nurse Cap still with you. Especially the last is very handy. Be careful with using Felix' Cure/Cure Well, as Felix doesn't have much PP already. Save those PP for Ragnarok (if you trained a lot) or Earthquake. If you are smart, try using the Mercury Djinni Fog so now and then, as he might affect your psynergy to. Use it for unleash, or to set on standby if you want your old psynergy back. Just do anything to keep yourself alive, to give damage and prepare for the next turn. Think carefully!

You know you can't fix everything by yourself now, but you could clean up at least 85% of the junk.
First, stand next to the log on the ship and use Move to move the stone into water, then push the log itself to the water. Jump on the frame of the mast and do the same on the other side, only this time with a box instead of a log. Walk on the rope, like displayed. Jump on the boat again and use Lash on the rope. Walk to the hill and climb downstairs. Pound the rope. Continue to the south and stand in FRONT of the box. MOVE the box to the left in the water.

Exit to the jail in Alhafra, which is extremely to the left of Alhafra. On your way to there, be sure to pick up a lucky medal between the two broken houses.
Oh yes, on your way to the jail, meet some little kid at the stairs who says he's extremely hungry. Give him the Large Bread you've found on the ship and he will tell you to go to the Alhafra Cave, between the jail and the Mayor's mansion. His father is guarding over there. If needed, repair some stuff at the shops, as your Nurse Cap might broke in battle (like happened with me). At least stock up with a few herbs or nuts. Then go to the jail, which is under the graveyards.

Enter the jail to figure out Briggs is certain to escape soon or later. You can notice that on behalf of Eoleo's power. Eoleo is the son of Briggs and it seems he can do psynergy, too. One of the seafighters see that and report it to Briggs. Briggs tries to stop Eoleo, but he will cry instead, making him and Chaucha, Briggs wife, leave. Exit the jail and go run uphill. Then take the path to west. Talk to the guy and he will permit you to go seek in the cave if you gave his son a Large Bread first.

Keep walking on the left and stay on the left all the time. After a door, you need to pound a pillar and use lash in order to get some cash, a lucky medal and the Ixion Mail. Walk all the way back to the exit, as you can't use retreat. Now it's time to meet the mayor.

The mayor lives in the big mansion on the hill. You'll figure out what he intents to do with Briggs and the ship. He's one big greedy bag and is very selfish. However, go to the tower in the southeast of his mansion to get a view of Airs Rock. Then leave the mansion and leave Alhafra. Be Sure to rest in the Inn (because of the fight with Briggs!)